Contain sets of codes to analyze Trajectory Surface Hopping dynamics data reproduced with Newton-X.
The details about each code are provided below:
Python Scripts
- collectblsandangles.py : This Python code convert XYZ coordinates of formaldehyde geometries at each time-step to the internal-coordinates(i.e. bond lengths, bond angles, and dihedrals). The code needs 'dyn.xyz' produced with Newton-X containing the geometries at each time-step. 'intcoors.txt' file is generated after successful execution of the code. Note- Play with the code ( a> change number of lines to be read = number of atoms of your molecule or b> Or just read the geometries of the atoms of interest) if wanting to implement this to your molecule.
SHELL Scripts
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copyfile.sh : A simple shell script to copy a file into each TRAJn folder inside TRAJECTORIES. Note - Replace 'cp' command with 'rm' command accordingly in order to remove files recursively.
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copynxslurm.sh : A more sophisticated version of the above code. It copies the slurm file into each TRAJn folder and then replaces the digit 906 with the TRAJ number. (Useful on HPCs)
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createdynxyz.sh : This shell script creates 'dyn.xyz' from dyn.out file inside TRAJn/RESULTS'.
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runjob.sh : This script submits the job inside each TRAJn folder. (useful on HPCs)
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finalstep.sh : Useful if wanting to check the final status of all the TRAJn at the same time.
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printcharges.sh : Useful if wanting to print charges in one file at the last time step of the dynamics.
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nxslurm.sh : The slurm file to run dynamics on EXPANSE (HPC).